Synthetic circuit designs for earth terraformation

BackgroundMounting evidence indicates that our planet might experience runaway effects associated to rising temperatures and ecosystem overexploitation, leading to catastrophic shifts on short time scales. Remediation scenarios capable of counterbalancing these effects involve geoengineering, sustainable practices and carbon sequestration, among others. None of these scenarios seems powerful enough to achieve the desired restoration of safe boundaries.Presentation of the hypothesisWe hypothesize that synthetic organisms with the appropriate engineering design could be used to safely prevent declines in some stressed ecosystems and help improving carbon sequestration. Such schemes would include engineering mutualistic dependencies preventing undesired evolutionary processes. We hypothesize that some particular design principles introduce unescapable constraints to the engineered organisms that act as effective firewalls.Testing the hypothesisTesting this designed organisms can be achieved by using controlled bioreactor models, with single and heterogeneous populations, and accurate computational models including different scales (from genetic constructs and metabolic pathways to population dynamics).Implications of the hypothesisOur hypothesis heads towards a future anthropogenic action that should effectively act as Terraforming processes. It also implies a major challenge in the existing biosafety policies, since we suggest release of modified organisms as potentially necessary strategy for success.ReviewersThis article was reviewed by This article was reviewed by Eugene V. Koonin, Tom Ellis (nominated by Purificación Lopez-Garcia) and Eörs Szathmary.

[1]  L. Amaral-Zettler,et al.  Life in the "plastisphere": microbial communities on plastic marine debris. , 2013, Environmental science & technology.

[2]  V. Lorenzo Recombinant bacteria for environmental release: what went wrong and what we have learnt from it. , 2009 .

[3]  K. Gross,et al.  Alternative states and positive feedbacks in restoration ecology. , 2004, Trends in ecology & evolution.

[4]  D. Barnes,et al.  Biodiversity: Invasions by marine life on plastic debris , 2002, Nature.

[5]  Neo D. Martinez,et al.  Approaching a state shift in Earth’s biosphere , 2012, Nature.

[6]  Michael Crichton,et al.  Jurassic Park , 1993, Bio/Technology.

[7]  Todd M. Scanlon,et al.  Positive feedbacks promote power-law clustering of Kalahari vegetation , 2007, Nature.

[8]  Ryo Takeuchi,et al.  Corrigendum: Biocontainment of genetically modified organisms by synthetic protein design , 2015, Nature.

[9]  Yi Y. Liu,et al.  Contribution of semi-arid ecosystems to interannual variability of the global carbon cycle , 2014, Nature.

[10]  M. Blaser,et al.  The human microbiome: at the interface of health and disease , 2012, Nature Reviews Genetics.

[11]  Jayne Belnap,et al.  The world at your feet: desert biological soil crusts , 2003 .

[12]  Y. Clough An Introduction to Methods and Models in Ecology, Evolution and Conservation Biology, S. Braude, B.S. Low. Princeton University Press, Princeton, Oxford (2010), 267 pp., £44.95 (cloth), £20.95 (paper), ISBN: 978-0-691-12723-1 (cloth), 978-0-691-12724-8 (paper) , 2011 .

[13]  Gerd H. G. Moe-Behrens,et al.  Preparing synthetic biology for the world , 2013, Front. Microbio..

[14]  George M Church,et al.  Concerning RNA-guided gene drives for the alteration of wild populations , 2014, bioRxiv.

[15]  Jeffrey E. Barrick,et al.  Engineering reduced evolutionary potential for synthetic biology. , 2014, Molecular bioSystems.

[16]  Timothy M. Lenton,et al.  A review of climate geoengineering proposals , 2011 .

[17]  M. Gregory Environmental implications of plastic debris in marine settings—entanglement, ingestion, smothering, hangers-on, hitch-hiking and alien invasions , 2009, Philosophical Transactions of the Royal Society B: Biological Sciences.

[18]  J. H. Langenheim Ecological Restoration Restoration Ecology: A Synthetic Approach to Ecological Research W. R. Jordan III M. E. Gilpin J. D. Aber , 1988 .

[19]  Richard V. Solé,et al.  Self-Organization in Complex Ecosystems. , 2006 .

[20]  Victor de Lorenzo,et al.  Genetically modified organisms for the environment: stories of success and failure and what we have learned from them. , 2005, International microbiology : the official journal of the Spanish Society for Microbiology.

[21]  J. Pepper,et al.  The emerging medical ecology of the human gut microbiome. , 2012, Trends in ecology & evolution.

[22]  Matthew A. Bowker,et al.  Functional profiles reveal unique ecological roles of various biological soil crust organisms , 2011 .

[23]  Katherine H. Huang,et al.  Structure, Function and Diversity of the Healthy Human Microbiome , 2012, Nature.

[24]  C. Médigue,et al.  Experimental evolution of nodule intracellular infection in legume symbionts , 2013, The ISME Journal.

[25]  Noah Alexander,et al.  Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics , 2015, Cell systems.

[26]  Alan Hastings,et al.  Ecological and evolutionary insights from species invasions. , 2007, Trends in ecology & evolution.

[27]  D. Simberloff,et al.  Encyclopedia of Biological Invasions , 2019 .

[28]  Richard J. Hobbs,et al.  Frontiers inEcology and the Environment Management of novel ecosystems : are novel approaches required ? , 2008 .

[29]  D. McCollum,et al.  Probabilistic cost estimates for climate change mitigation , 2013, Nature.

[30]  Kenneth E. F. Watt,et al.  Systems Analysis in Ecology , 1967 .

[31]  Martin Fussenegger,et al.  Emerging biomedical applications of synthetic biology , 2011, Nature Reviews Genetics.

[32]  Nitin S. Baliga,et al.  Erosion of functional independence early in the evolution of a microbial mutualism , 2014, Proceedings of the National Academy of Sciences.

[33]  A. Thomas,et al.  Extracellular polysaccharides from cyanobacterial soil crusts: A review of their role in dryland soil processes , 2011 .

[34]  R. L. Kitching Systems Ecology: An Introduction to Ecological Modelling , 1983 .

[35]  Michael E. Gilpin,et al.  Restoration Ecology: A Synthetic Approach to Ecological Research , 1989 .

[36]  Jayne Belnap,et al.  Microbial colonization and controls in dryland systems , 2012, Nature Reviews Microbiology.

[37]  Ahmad S. Khalil,et al.  Synthetic biology: applications come of age , 2010, Nature Reviews Genetics.

[38]  M. Scheffer,et al.  Slow Response of Societies to New Problems: Causes and Costs , 2003, Ecosystems.

[39]  K. Caldeira,et al.  The Science of Geoengineering , 2013 .

[40]  Erle C. Ellis,et al.  Used planet: A global history , 2013, Proceedings of the National Academy of Sciences.

[41]  V. de Lorenzo,et al.  Systems biology approaches to bioremediation. , 2008, Current opinion in biotechnology.

[42]  J. Lawton,et al.  Organisms as ecosystem engineers , 1994 .

[43]  Ricard Sol'e,et al.  Bioengineering the biosphere , 2014, 1410.8708.

[44]  Andrew W. Murray,et al.  Genetic drift opposes mutualism during spatial population expansion , 2014, Proceedings of the National Academy of Sciences.

[45]  Marten Scheffer,et al.  Critical Transitions in Nature and Society , 2009 .

[46]  B. Glavovic,et al.  Adapting to Climate Change: Lessons from Natural Hazards Planning , 2013 .

[47]  Danièle Revel,et al.  IPCC Special Report on Renewable Energy Sources and Climate Change Mitigation , 2011 .

[48]  Ricard Solé,et al.  Ecology: Scaling laws in the drier , 2007, Nature.

[49]  Emily E. Peacock,et al.  Plastic Accumulation in the North Atlantic Subtropical Gyre , 2010, Science.

[50]  J. Belnap,et al.  Biological Soil Crusts: Structure, Function, and Management , 2003, Ecological Studies.

[51]  C. Médigue,et al.  Experimental Evolution of a Plant Pathogen into a Legume Symbiont , 2010, PLoS biology.

[52]  Johan van de Koppel,et al.  Regular pattern formation in real ecosystems. , 2008, Trends in ecology & evolution.

[53]  Deborah J. Roberts,et al.  Isolation and characterization of microorganisms involved in the biodeterioration of concrete in sewers , 2000 .

[54]  Wenying Shou,et al.  Synthetic cooperation in engineered yeast populations , 2007, Proceedings of the National Academy of Sciences.

[55]  Erik F. Y. Hom,et al.  Niche engineering demonstrates a latent capacity for fungal-algal mutualism , 2014, Science.

[56]  Stephen H Schneider,et al.  Geoengineering: could we or should we make it work? , 2008, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.

[57]  S. Carpenter,et al.  Catastrophic shifts in ecosystems , 2001, Nature.

[58]  S. West,et al.  Reciprocal Rewards Stabilize Cooperation in the Mycorrhizal Symbiosis , 2011, Science.

[59]  D. Relman,et al.  The Application of Ecological Theory Toward an Understanding of the Human Microbiome , 2012, Science.

[60]  M. Rietkerk,et al.  Spatial vegetation patterns and imminent desertification in Mediterranean arid ecosystems , 2007, Nature.

[61]  R. Ruess,et al.  Cycling Dynamics of NH4+ and Amino Acid Nitrogen in Soils of a Deciduous Boreal Forest Ecosystem , 2002, Ecosystems.

[62]  S. Levin Ecosystems and the Biosphere as Complex Adaptive Systems , 1998, Ecosystems.

[63]  Ricard V. Solé,et al.  Self-Organization in Complex Ecosystems. (MPB-42) , 2006 .

[64]  M. Sogin,et al.  Sewage Reflects the Microbiomes of Human Populations , 2015, mBio.

[65]  David William Keith Geoengineering the Climate: History and Prospect 1 , 2000, The Ethics of Nanotechnology, Geoengineering and Clean Energy.

[66]  S. Carpenter,et al.  Multiscale regime shifts and planetary boundaries. , 2013, Trends in ecology & evolution.

[67]  Michael D. Ward Scaling laws in the drier , 2007 .

[68]  J. Lawton,et al.  POSITIVE AND NEGATIVE EFFECTS OF ORGANISMS AS PHYSICAL ECOSYSTEM ENGINEERS , 1997 .

[69]  M. Bowker Biological Soil Crust Rehabilitation in Theory and Practice: An Underexploited Opportunity , 2007 .

[70]  J. Hur,et al.  Effects of Superabsorbent Polymer on Cyanobacterial Biological Soil Crust Formation in Laboratory , 2015 .

[71]  J. Travis,et al.  Facilitation in plant communities: the past, the present, and the future , 2007 .

[72]  Ryo Takeuchi,et al.  Biocontainment of genetically modified organisms by synthetic protein design , 2015, Nature.

[73]  G. Muyzer,et al.  Application of bacteria as self-healing agent for the development of sustainable concrete , 2010 .